I don't know if this can be called a bug. It's a situation I have encountered and how I have solved it.
In 4.0.5, I was using Putty (with CTRL-P) directly from WinSCP. Then, I tried using 4.1.3 and copied the .ini, but CTRL-P was not working.
So I removed this line from my winscp .ini file :
And now it works.
WinSCP 4.1.3 recreated that entry with the following value.